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- PDB-8vxg: The crystal structure of CYP125MRCA, an ancestrally reconstructed... -

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Basic information

Entry
Database: PDB / ID: 8vxg
TitleThe crystal structure of CYP125MRCA, an ancestrally reconstructed CYP125 enzyme
ComponentsCYP125MRCA
KeywordsLIPID BINDING PROTEIN / P450 / Cytochrome / Enzyme / Heme / Steroid / Vitamin D3 / cholecalciferol / CYP125 / Ancestor
Function / homologyPROTOPORPHYRIN IX CONTAINING FE / ISOPROPYL ALCOHOL / Chem-VD3
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsDoherty, D.Z. / Bruning, J.B. / Bell, S.G.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP210103970 Australia
CitationJournal: Chem Sci / Year: 2025
Title: Evolutionary insights into the selectivity of sterol oxidising cytochrome P450 enzymes based on ancestral sequence reconstruction.
Authors: Doherty, D.Z. / De Voss, J.J. / Bruning, J.B. / Bell, S.G.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYP125MRCA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47810
Polymers48,0871
Non-polymers1,3919
Water5,585310
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.591, 118.486, 94.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-812-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CYP125MRCA


Mass: 48086.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 319 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-VD3 / (1S,3Z)-3-[(2E)-2-[(1R,3AR,7AS)-7A-METHYL-1-[(2R)-6-METHYLHEPTAN-2-YL]-2,3,3A,5,6,7-HEXAHYDRO-1H-INDEN-4-YLIDENE]ETHYLI DENE]-4-METHYLIDENE-CYCLOHEXAN-1-OL / VITAMIN D3


Mass: 384.638 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H44O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 4000, 20% isopropanol, 0.1 M Sodium citrate tribasic trihydrate
PH range: 5.2 -5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953658521175 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953658521175 Å / Relative weight: 1
ReflectionResolution: 1.78→47.41 Å / Num. obs: 39392 / % possible obs: 99.6 % / Redundancy: 13.3 % / CC1/2: 0.998 / Net I/σ(I): 10.4
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 2063 / CC1/2: 0.64

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→37.638 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1989 5.06 %
Rwork0.1734 --
obs0.1757 39293 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→37.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 25 310 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073394
X-RAY DIFFRACTIONf_angle_d1.0954617
X-RAY DIFFRACTIONf_dihedral_angle_d5.4472815
X-RAY DIFFRACTIONf_chiral_restr0.053481
X-RAY DIFFRACTIONf_plane_restr0.005614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.82430.28611350.26752438X-RAY DIFFRACTION92
1.8243-1.87360.26631330.23282655X-RAY DIFFRACTION100
1.8736-1.92870.27631450.20872663X-RAY DIFFRACTION100
1.9287-1.9910.23781390.19222623X-RAY DIFFRACTION100
1.991-2.06210.23971400.19052660X-RAY DIFFRACTION100
2.0621-2.14470.24781500.18462629X-RAY DIFFRACTION100
2.1447-2.24230.22561400.17452678X-RAY DIFFRACTION100
2.2423-2.36050.23021400.17092654X-RAY DIFFRACTION100
2.3605-2.50830.21491410.17622675X-RAY DIFFRACTION100
2.5083-2.7020.21521510.1822662X-RAY DIFFRACTION100
2.702-2.97380.25471420.1812687X-RAY DIFFRACTION100
2.9738-3.40380.20871440.17212704X-RAY DIFFRACTION100
3.4038-4.28750.19131370.14782741X-RAY DIFFRACTION100
4.2875-37.6380.19021520.15792835X-RAY DIFFRACTION100

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